Is overlapping but not connected geometry bad?
Should you avoid it? Yes.
Does it necessarily look bad?
It depends on the direction of the normals of the two overlapping faces.
If the normals are facing the same way you might have some bizarre results in Unity or other game engines. If they're facing different ways and you're using a 1 sided material shader it's not going to look wrong, just 2 sided, and you might not even notice it because a side would be on the inside, and if one only cares about triangle/face count it's totally ignorable.
Anyway, yes, as I said, do avoid overlapping things if you can.